Super-enhancer lncRNA (SE-lncRNAs) are a special set of long noncoding RNAs transcribed from super-enhancer genomic loci. SE-lncRNAs play fundamental roles coupled to the active super-enhancers to regulate the gene expression programs that determine the cell lineages and identities. SE-lncRNA have been associated with many human diseases and their expression manifests in profound phenotypic changes [1-3]. Arraystar has developed the first commercially available SE-lncRNA Arrays for human, mouse, and rat to comprehensively, systematically and sensitively profile the SE-lncRNAs and their cis- or trans-regulated coding genes on the same array. The microarray profiling service is provided from RNA sample to analyzed data. The SE-lncRNA profiling is essential to study the super-enhancer activities, mechanisms, functions and diseases.
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2. Alvarez-Dominguez JR, Knoll M, Gromatzky AA, Lodish HF: The Super-Enhancer-Derived alncRNA-EC7/Bloodlinc Potentiates Red Blood Cell Development in trans. Cell Rep 2017, 19(12):2503-2514.[PMID: 28636939]
3. Xiang JF et al: Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res 2014, 24(5):513-531.[PMID: 24662484]
4. Vucicevic D et al: Long ncRNA expression associates with tissue-specific enhancers. Cell Cycle 2015, 14(2):253-260.[PMID: 25607649]
5. Hon CC et al: An atlas of human long non-coding RNAs with accurate 5' ends. Nature 2017, 543(7644):199-204.[PMID: 28241135]
6. Soibam B: Super-lncRNAs: identification of lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation. RNA 2017, 23(11):1729-1742.[PMID: 28839111]
Powerful SE-lncRNA collection
• LncRNA foundation using Arraystar premium transcriptome and lncRNA databases for comprehensive, high quality systematic lncRNA compilation.
- Reliable lncRNAs comprehensively sourced from public databases, such as Refseq, UCSC knownGene, GENCODE, lncRNAdb, RNAdb, NRED and lncRNA Catalogs.
- Gold standard lncRNAs for well annotated, experimentally studied and Pubmed indexed lncRNAs.
- Manual curation of lncRNAs from continuous scientific publication review and selection.
• Super-enhancer regions are cataloged in the dbSUPER database.
• SE-lncRNAs are identified by mapping the lncRNAs to the super-enhancer regions.
Simultaneous profiling of SE-lncRNAs and their target genes on the same array, to experimentally observe, quantify, correlate and establish accurate regulatory relationships.
SE-lncRNAs transcript isoforms are unambiguously, specifically and reliably detected by unique exon or splice-junction array probes (Fig. 1), with high sensitivity at one transcript per cell.
Figure 1. The unique sequence of Probe #2’ specifically detects lncRNA CCAT1-L isoform.
Detailed annotation for super-enhancers, SE-lncRNAs and their associated target coding genes.
Figure 2. A snippet of comprehensive SE-lncRNA annotations. TransID, SE-lncRNA's transcript ID; Gene symbol, SE-lncRNA's gene symbol; Alias, SE-lncRNA's gene symbol alias; Locus, SE-lncRNA's genomic locus(HG19); Subcellular Localization, SE-lncRNA's subcellular localization; Level, SE-lncRNA's annotation in ArrayStar's Human lncRNA Array; Associated cell or tissue, SE-lncRNA assocaited cell or tissue types from the FANTOM5 CAT annotation; Cancer, experimentally supported associations between lncRNA and human cancer from the database Lnc2Cancer; Disease, experimentally supported lncRNA-disease association from the database LncRNADisease; Super-LncRNA, lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation from Benjamin Soibam et al, 2017; SeqLength; the length of the SE-lncRNA sequence; Sequence, the dna sequence of the SE-lncRNA; Overlapped superenhancer information, information of dbSUPER's super enhancers overlapped with SE-lncRNA; Associated Gene, the ENSEMBL protein-coding genes overlapped with SE-lncRNA or closest to SE-lncRNA; Overlapped Gene symbol, the gene symbol of the genes overlapped with SE-lncRNAs; Overlapped Gene ID, the gene id of the genes overlapped with SE-lncRNAs; Proximal Gene symbol, the gene symbol of the genes closest to SE-lncRNAs; Proximal Gene ID, the gene id of the genes closest to SE-lncRNAs.
Arraystar's specially-designed SE-LncRNA Arrays are available only through our SE-LncRNA Array service. We provide full-service SE-LncRNA Array profiling, from sample preparation to in-depth data analysis. Our step-by-step quality controls are designed to ensure you get the most reliable results. Just send us your samples, and we'll do the rest!
Please refer to Sample Submission for details in how to get your project started.
• RNA isolation (Optional)
• RNA QC
• cDNA synthesis
• Target preparation by efficient labeling with Cy3
• Array hybridization, washing, and scanning
• Data extraction, analysis and summarization